Main description:

This book details the development of methods and models to study the HIV-1 viral reservoir with the ultimate goal of achieving a functional cure of HIV infection. Chapters are divided into six parts covering cell lines, in vitro and ex vivo primary cell models of persistent infection, in vitro and ex vivo tissue-derived models, infected animal models human immune cells, methods of detection and analysis of the reservoir, and current approaches to achieve either a functional cure or cART-free long-term remission. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

Authoritative and cutting-edge, HIV Reservoirs: Methods and Protocols provides a comprehensive, updated collection of state-of-art methodologies and models to tackle the HIV-1 viral reservoir.

Contents:

Part I: Cell lines with Minimal but Inducible Proviral Expression

1. Jurkat-derived (J-Lat, J1.1 and Jurkat E4) and CEM-derived T cell lines (8E5, ACH-2) as Models of Reversible Proviral Latency

Anthony RODARI, Guido Poli, and Carine VAN LINT

2. U1 and OM10.1. Myeloid Cell Lines as Surrogate Models Of Reversible Proviral Latency

Guido Poli

Part II: In vitro and ex vivo primary cell models of minimal but inducible proviral expression

3. An In Vitro System to Model the Establishment and Reactivation of HIV-1 Latency

in primary human CD4+ T cells

Rui Li and Fabio Romerio

4. The cultured TCM model of HIV latency

Alberto Bosque

5. A Reliable Primary Cell Model for HIV latency: The QUECEL (Quiescent Effector Cell Latency) MethodMeenakshi Shukla, Fredrick Kizito, Uri Mbonye, Kien Nguyen, Curtis Dobrowolski, and Jonathan Karn

6. TGF-b signaling supports HIV latency in a Memory CD4+ T cell based in vitro model

Sydney Bergstresser and Deanna A. Kulpa

7. Flow Cytometry Sorting of Memory CCR6+CD4+ T-Cells for HIV Reservoirs Quantification

Amelie Cattin, Augustine Fert, Delphine Planas, and Petronela Ancuta

8. Human monocyte-derived macrophages (MDM) - Model 1 (GM-CSF)

Claudia Alteri, Lorenzo Piermatteo, Francesca Ceccherini Silberstein, Valentina Svicher, and Carlo Federico Perno

9. Human monocyte-derived macrophages (MDM) - Model 2

Francesca Graziano, Elisa Vicenzi, and Guido Poli

10. Modeling HIV latency in astrocytes with the human neural progenitor cell line HNSC.100

Amelie Bauer

11. Hematopoietic stem and progenitor cells (HSPCs)

Valeri H. Terry, Gretchen E. Zimmerman, Maria C. Virgilio, Mark M. Painter, Dale Bixby, and Kathleen L. Collins

Part III: In vitro and ex vivo tissue-derived models of reversible proviral latency

12. HIV reservoirs: Modeling, Quantification and Approaches to a Cure

Louise A. Ouattara, Nikolas C. Vann, and Gustavo F. Doncel

13. More than a gender issue: Testis as a distinctive HIV reservoir and its implication for viral eradication

Jean-Pierre Routy, Franck P. Dupuy, John Lin, and Stephane Isnard

Part IV: Animal Models

14. Experimental Models to Study HIV Latency Reversal from Male Genital Myeloid Cells

Fernando Real, Yonatan Ganor, and Morgane Bomsel

15. Decidua basalis: An ex vivo Model to Study HIV-1 Infection during Pregnancy and Beyond

Nabila Jabrane-Ferrat and Hicham El Costa

16. HIV Reservoirs: Modeling, Quantification, and Approaches to a Cure

Amir Dashti, Vidisha Singh, and Ann Chahroudi

17. Human Hematopoietic Stem Cell (HSC)-Engrafted NSG Mice for HIV Latency Research

Triana Rivera-Megias, Nhut M Le, and Alonso Heredia

18. Inducing long-term HIV-1 latency in the TKO-BLT mouse model

Yunyun Di and Kerry J. Lavender

Part V: Methods for detection and analysis of the reservoir

19. In situ multiplexing to identify, quantify, and phenotype the HIV-1/SIV reservoir within lymphoid tissue

Kathleen Busman-Sahay, Michael D. Nekorchuk, Carly Elizabeth Starke, Chi Ngai Chan, and Jacob D. Estes

20. Single-cell multiparametric analysis of rare HIV-infected cells identified by duplexed RNAflow-FISH

Mathieu Dube and Daniel E. Kaufmann

21. Ex vivo differentiation of resting CD4+ T lymphocytes enhances detection of replication competent HIV-1 in viral outgrowth assays

Elizabeth R. Wonderlich, Monica D. Reece, and Deanna A. Kulpa

22. Quantitative Viral Outgrowth Assay to Measure the functional SIV Reservoir in Myeloid Cells

Abreu CM, Veenhuis RT, Shirk EN, Queen SE, Bullock BT, Mankowski JL, Gama L and Clements JE

23. Near-full-length single-genome HIV-1 DNA sequencing

Guinevere Q. Lee and Mathias Lichterfeld

24. TILDA: Tat/rev Induced Limiting Dilution Assay

Cynthia Lungu and Francesco A. Procopio

Part VI: Cure and long-term remission strategies

25. Latency Reversal and Clearance of Persistent HIV Infection

David M. Margolis

26. Cure and long-term remission strategies

Luisa Mori and Susana T. Valente

27. Pathways Toward a Functional HIV-1 Cure: Balancing Promise and Perils for CRISPR Therapy

Jonathan Herskovitz, Mahmudul Hasan, Milankumar Patel, Bhavesh D Kevadiya,and Howard E. Gendelman